Examples with ExpressionExperiment ubic.gemma.model.expression.experiment.ExpressionExperiment used on opensource projects

Example 46 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class GeoSuperSeriesLoadTest method tearDown.

@After
public void tearDown() {
    if (ee != null) {
        try {
            this.removeOldData(ee);
        } catch (Exception e) {
            log.warn("Removing expression experiment thew an Exception");
        }
    }
    // this is somewhat overkill...
    for (ExpressionExperiment ee4 : ees.loadAll()) {
        try {
            ees.remove(ee4);
        } catch (Exception e) {
            log.warn("Removing all expression experiments thew an Exception");
        }
    }
    for (ArrayDesign a : adService.loadAll()) {
        try {
            a = adService.thawLite(a);
            for (ArrayDesign b : a.getSubsumedArrayDesigns()) {
                adService.remove(b);
            }
            adService.remove(a);
        } catch (Exception e) {
            log.warn("Removing all array designs thew an Exception");
        }
    }
}

Example 47 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class TwoChannelMissingValuesTest method testMissingValueGSE56.

/**
 * GSE56 is corrupt: there is no Channel 1 signal value in the data file.
 */
@Test
public void testMissingValueGSE56() throws Exception {
    ExpressionExperiment old = eeService.findByShortName("GSE56");
    if (old != null)
        eeService.remove(old);
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE56Short/GSE56_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE56");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    ExpressionExperiment expExp = (ExpressionExperiment) ((Collection<?>) result).iterator().next();
    expExp = persisterHelper.persist(expExp, persisterHelper.prepare(expExp));
    Collection<RawExpressionDataVector> calls = tcmv.computeMissingValues(expExp, 2.0, new ArrayList<Double>());
    assertEquals(10, calls.size());
}

Example 48 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class TwoChannelMissingValuesTest method testMissingValue.

@Test
public void testMissingValue() throws Exception {
    ExpressionExperiment old = eeService.findByShortName("GSE2221");
    if (old != null)
        eeService.remove(old);
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/shortGenePix/GSE2221_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE2221");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    ExpressionExperiment expExp = (ExpressionExperiment) ((Collection<?>) result).iterator().next();
    expExp = persisterHelper.persist(expExp, persisterHelper.prepare(expExp));
    Collection<RawExpressionDataVector> calls = tcmv.computeMissingValues(expExp, 2.0, new ArrayList<Double>());
    assertEquals(500, calls.size());
    BioAssayDimension dim = calls.iterator().next().getBioAssayDimension();
    // Spot check the results. For sample ME-TMZ, ID #27 should be 'true' and 26 should be false.
    ByteArrayConverter bac = new ByteArrayConverter();
    boolean foundA = false;
    boolean foundB = false;
    for (DesignElementDataVector vector : calls) {
        if (vector.getDesignElement().getName().equals("26")) {
            byte[] dat = vector.getData();
            boolean[] row = bac.byteArrayToBooleans(dat);
            int i = 0;
            for (BioAssay bas : dim.getBioAssays()) {
                if (bas.getName().equals("expression array ME-TMZ")) {
                    assertTrue(!row[i]);
                    foundA = true;
                }
                i++;
            }
        }
        if (vector.getDesignElement().getName().equals("27")) {
            byte[] dat = vector.getData();
            boolean[] row = bac.byteArrayToBooleans(dat);
            int i = 0;
            for (BioAssay bas : dim.getBioAssays()) {
                if (bas.getName().equals("expression array ME-TMZ")) {
                    assertTrue(row[i]);
                    foundB = true;
                }
                i++;
            }
        }
    }
    assertTrue(foundA && foundB);
}

Example 49 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class TwoChannelMissingValuesTest method testMissingValueGSE5091.

/**
 * GSE56 is corrupt: there is no Channel 1 signal value in the data file.
 */
@Test
public void testMissingValueGSE5091() throws Exception {
    ExpressionExperiment old = eeService.findByShortName("GSE5091");
    if (old != null)
        eeService.remove(old);
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE5091Short/GSE5091_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE5091");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    gc = this.getBean(GeoConverter.class);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    ExpressionExperiment expExp = (ExpressionExperiment) ((Collection<?>) result).iterator().next();
    expExp = persisterHelper.persist(expExp, persisterHelper.prepare(expExp));
    Collection<RawExpressionDataVector> calls = tcmv.computeMissingValues(expExp, 2.0, new ArrayList<Double>());
    assertEquals(10, calls.size());
}

Example 50 with ExpressionExperiment

use of ubic.gemma.model.expression.experiment.ExpressionExperiment in project Gemma by PavlidisLab.

the class BatchInfoPopulationServiceIntegrationTest method testLoad.

@Test
public void testLoad() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath()));
    ExpressionExperiment newee;
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE26903", false, true, false);
        newee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        newee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
    }
    assertNotNull(newee);
    newee = eeService.thawLite(newee);
    assertTrue(batchInfoPopulationService.fillBatchInformation(newee, true));
}